Vesicular stomatitis virus (VSV), the prototypic Rhabdovirus, has a non-segmented negative-sense (ns NS or NNS) RNA genome of 11,161 nucleotides comprising a 50-nucleotide 3′ leader region (Le); five genes that encode the viral nucleocapsid (N) protein, phosphoprotein (P), matrix (M) protein, attachment glycoprotein (G) and large polymerase subunit (L), and a 59-nucleotide trailer region (Tr), arranged in the order 3′-Le-N-P-M-G-L-Tr 5′ (1, 3, 4). The viral genomic RNA is encapsidated by N protein to form a ribonuclease-resistant ribonucleoprotein (RNP) complex that acts as template for the RNA-dependent RNA polymerase (RdRP). The viral components of the RdRP are a monomer of the 241-kDa L protein and a trimer of the 29-kDa P protein (19). During RNA synthesis, the RdRP uses the encapsidated genomic RNA as template in two distinct reactions: (i) transcription of five messenger RNAs that encode the N, P, M, G and L proteins; and (ii) replication to yield full length antigenomic and then genomic strands (reviewed in ref. 66).
During transcription the RdRP sequentially synthesizes five capped and polyadenylated mRNAs (1, 3, 4). These mRNAs are not produced in equimolar amounts; rather, their abundance decreases with distance from the 3′ end of the template such that N>P>M>G>L (63). This polarity gradient reflects a localized transcriptional attenuation at each gene junction, where 30% of RdRP molecules fail to transcribe the downstream gene (34). The widely accepted model for mRNA synthesis is the stop-start model of sequential transcription. In the original version of this model, polymerase initiates at a single site on the genome yielding a leader RNA and, by sequential reinitiation, the 5 viral mRNA's. Access of polymerase to downstream genes is, therefore, entirely dependent upon termination of transcription of the upstream gene (hence stop-start). Recent experiments with VSV indicate that the polymerase molecule that transcribes the leader region does not proceed to transcribe the N mRNA (12, 46, 67). Other than this refinement, the stop-start model is well supported by much experimental evidence (reviewed in 66).
The cap structure of ns NS viral mRNAs is formed by a mechanism that appears unique. For VSV (2), respiratory syncytial virus (7) and spring viremia of carp virus (26), the two italicized phosphates of the 5′Gppp5′NpNpN triphosphate bridge have been shown to be derived from a GDP donor. By contrast, cellular and all other known viral capping reactions involve GMP transfer (reviewed in 24). This difference, combined with the cytoplasmic location of viral RNA synthesis suggested that a viral protein, possibly the L protein subunit of polymerase, possesses guanylyltransferase activity, though direct evidence for this is lacking. Following capping, the 5′ terminus of the nascent transcript is methylated by [guanine-N-7] and [ribose-2′-O] methyltransferases (30, 35, 40, 41, 48-50, 62). These activities have been mapped to the L gene (30). Recent work has shown that alteration of amino acid residue D1671 which resides within a predicted s-adenosyl methionine (SAM) binding region of L protein inhibited mRNA cap methylation (25). However, the catalytic residues within the polymerase, the substrate requirements for the reactions and the order in which the mRNA processing reactions occur, remain poorly understood.
The nucleotide sequence of 39 ns NS RNA virus genomes have been determined. See “The Viral Genomes Resources” Homepage at NCBI. Amino acid sequence alignments between the L proteins of representative members of each family identified 6 conserved domains numbered I-VI (45). X-ray crystal structures of representative members of each class of template-dependent polynucleotide polymerase have been determined. Each contains a catalytic core resembling a cupped right hand. Within the palm region are motifs A-B-C-D found in all polymerases and motif E, found in RdRPs and reverse transcriptase. Domain III of the ns NS virus L proteins contains these A-B-C-D motifs. Consistent with this, domain III of VSV L was shown to be critical for polymerase activity (58). Functions have yet to be assigned to the other conserved domains, although sequence comparisons to FtsJ/RrmJ (FIG. 1), a heat shock methyltransferase of Escherichia coli, suggest that a region spanning domain VI might function as a [ribose-2′-O]-methyltransferase (9, 22).
A comprehensive genetic and biochemical analysis of the conserved domains of the VSV L protein has not been performed. However, studies with the paramyxovirus, Sendai (SeV), showed that genetic alterations introduced throughout each of the conserved domains of L protein revealed multiple defects in a reconstituted RNA synthesis assay (11, 20, 21, 32, 59, 60). These studies did not permit the assignment of specific functions to conserved domains of L protein. Rather, these experiments indicated that the global architecture of the SeV L protein was essential for all polymerase functions. More recently, domains V and VI of the SeV L protein were expressed independently and shown to retain the ability to methylate short RNA's that correspond to the 5′ end of SeV mRNA (43). The ability to functionally separate a domain of the SeV L is consistent with studies of measles virus (MV), in which the coding sequence of green fluorescent protein was inserted at two positions within L protein (17). The resulting polymerase was functional, suggesting that the MV L protein folds and functions as a series of independent globular domains (17).
The NNS RNA viruses include some of the most significant human, animal and plant pathogens extant. For many of these viruses there are no vaccines or efficacious antiviral drugs. The development of effective vaccines against such viruses is an ongoing need.